Harvard:Biophysics 101/2007/Project: Difference between revisions

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= Overview =
*Project Goal: Development of tools to aid in analysis of personal DNA sequences. 
<pre>
We would like to develop software and documentation that will help people get from sequence to diagnosis.  At the moment, we are focusing on identifying and classifying SNPs, but we will broaden this identification to other things like large deletions or insertions or repeats when we have more expertise.  We are attempting to harness the power of other already existing tools, and we would also like to make this tool one that others can build upon.  Specifically, our program will eventually be able to determine location based on BLAST, determine any SNPs based on NCBI SNP, and give a prognosis based on OMIM and online medical databases.
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=Project Sections=
=Project Sections=
* ATTENTION: Everyone needs to post their code to one place.  Let's say everyone post a link from here that works to their code and then I'll be able to combine it all. --[[User:Kfifer|Katie Fifer]]
* ATTENTION: Everyone needs to post their code to one place.  Let's say everyone post a link from here that works to their code and then I'll be able to combine it all. --[[User:Kfifer|Katie Fifer]]

Revision as of 05:50, 22 March 2007

Biophysics 101: Genomics, Computing, and Economics

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Overview

  • Project Goal: Development of tools to aid in analysis of personal DNA sequences.
We would like to develop software and documentation that will help people get from sequence to diagnosis.  At the moment, we are focusing on identifying and classifying SNPs, but we will broaden this identification to other things like large deletions or insertions or repeats when we have more expertise.  We are attempting to harness the power of other already existing tools, and we would also like to make this tool one that others can build upon.  Specifically, our program will eventually be able to determine location based on BLAST, determine any SNPs based on NCBI SNP, and give a prognosis based on OMIM and online medical databases.

Project Sections

  • ATTENTION: Everyone needs to post their code to one place. Let's say everyone post a link from here that works to their code and then I'll be able to combine it all. --Katie Fifer
  • Could someone who typed this up today please add the other sections that are being worked on? --TChan, 12:47 20 March 2007
  • The following is from the information that Zach typed up in class (Located here) --Hetmann, 5:32 20 March 2007

OMIM Parsing

  • Resmi, Cynthia, and Hetmann

BLAST SNP to OMIM

  • Zach, Mike, and Tiffany

BioPython Modification

  • Modifying BioPython BLAST

Parsing XML from #2 in python

  • Deniz
  • OMIM download

Integration

  • Katie
  • PM / encourage documentation

OMIM XML Parse

  • Xiaodi - completed?
  • rs-->OMIM XML parse -> phenotype text


Chris

  • if one gets multiple SNPs, which is revelant?
  • linking to PubMED after finding disease

Kay

Beyond OMIM

  • Tiffany, Resmi, Deniz, Xiaodi, Mike (note: ask if API exists)

Unassigned

  1. not in SNP db... then what? - I'd like to point out new efforts that aim to replace OMIM, called the "Human Variome Project" -- Deniz
  2. OMIM DOA
  3. systematically nonsyn. -> mutation not in OMIM or dbSNP?
  4. other dbs: genecard (spec. conservation, pop. freq)
  5. looking into linking gene expression w/ GEO?

Project Ideas

Project ideas have been moved to their own page.

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